Is there something in R to open a text file? In Python, one could open a text file using notepad:
import subprocess as sp
programName = "notepad.exe"
fileName = "file.txt"
sp.Popen([programName, fileName])
Other methods are described in the post as well. Is there something similar in R?
Keeping in mind portability issues, i.e. this is specific to Windows, you can use shell.exec, which will open the file in whatever program is associated with that type of file by default - e.g.
## full path
shell.exec(paste0(c(getwd(), "/tmpfile.txt"),collapse = ""))
## relative to current working directory
shell.exec("tmpfile.txt")
both open tmpfile.txt in notepad on my machine.
Related
I create a text file below:
myFile<-file("toGoogle.txt")
writeLines(c("InternetShortcut]","URL=http://www.google.com","IconFile=http://www.google.com/favicon.ico",
"IconIndex=0"), myFile)
close(myFile)
For clarity the text file now contains the following:
[InternetShortcut]
URL=http://www.google.com
IconFile=http://www.google.com/favicon.ico
IconIndex=0
In Windows, if I manually rename the file to "toGoogle.url" I am prompted:
After saying "Yes" the file is now a usable web link:
However when I use file.rename or any other substitute in R to change the file extension of toGoogle.txt it creates a dead web link with a target of "".
Is there a simple way out there to create a web shortcut using R? Or how can I change the file extension in R in a way that Windows is going to recognize it?
Edit: Using R to make the url weblink gives this:
And opening it prompts me with this:
The function file.rename works for me. And why not use file("toGoogle.url") to create a .url file directly.
I have an excel file that I want to open in R. I tried both of these commands after saving the excel file as a csv file or a text file.
read.table() or read.csv()
I think part of the problem is where the file is located. I have it saved on the desk top. What am I missing here?
Here is the R output
In file(file, "rt") :
cannot open file 'Rtrial.csv': No such file or directory
> help.search("read.csv")
> read.csv("Rtrial.csv")
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
cannot open file 'Rtrial.csv': No such file or directory
> read.table("tab")
To throw out another option, why not set the working directory (preferably via a script) to the desktop using setwd('C:\John\Desktop') and then read the files just using file names
Try
f <- file.choose()
to choose the file interactively and save the name in f.
Then run read.csv on the saved filename
d <- read.csv(f)
Sound like you just have an issue with the path. Include the full path, if you use backslashes they need to be escaped: "C:\\folder\\folder\\Desktop\\file.csv" or "C:/folder/folder/Desktop/file.csv".
myfile = read.csv("C:/folder/folder/Desktop/file.csv") # or read.table()
It may also be wise to avoid spaces and symbols in your file names, though I'm fairly certain spaces are OK.
I had to combine Maiasaura and Svun answers to get it to work: using setwd and escaping all the slashes and spaces.
setwd('C:\\Users\\firstname\ lastname\\Desktop\\folder1\\folder2\\folder3')
data = read.csv("file.csv")
data
This solved the issue for me.
Here is one way to do it. It uses the ability of R to construct file paths based on the platform and hence will work on both Mac OS and Windows. Moreover, you don't need to convert your xls file to csv, as there are many R packages that will help you read xls directly (e.g. gdata package).
# get user's home directory
home = setwd(Sys.getenv("HOME"));
# construct path to file
fpath = file.path(home, "Desktop", "RTrial.xls");
# load gdata library to read xls files
library(gdata);
# read xls file
Rtrial = read.xls(fpath);
Let me know if this works.
Save as in excel will keep the file open and lock it so you can't open it. Close the excel file or you won't be able to use it in R.
Give the full path and escape backslashes read.csv("c:\\users\\JoeUser\\Desktop\\JoesData.csv")
I have experienced that this error occurs when you either move the excel file to the destination other than where your r file is located or when you move your r file to the destination other than where your excel file is located.
Good Practice:
Keep your .r and .csv files in the same directory.
open your .r file from getting into its directory instead of opening the r file from rstuio's open file option.
You also have import Dataset option at Environment Block, just click there and get your required packages installed & from next time use this option to read datasets. You will not get this error again.
I also appreciate the above provided answers.
Another way of reading Excel including the new format xlsx could be the package speedR (https://r-forge.r-project.org/projects/speedr/). It is an interactive and visual data importer. Besides importing you can filter(subset) the existing objects from the R workspace.
My issue was very simple, the working directory was not the "Source" directory that was printed when the file ran. To fix this, you can use getwd() and setwd() to get your relative links working, or just use a full path when opening the csv.
print(getwd()) # Where does the code think it is?
setwd("~/Documents") # Where do I want my code to be?
dat = read.csv("~/Documents/Data Visualization/expDataAnalysis/one/ac1_survey.csv") #just make it work!
MAC OS It happened to me as well. I simply chose from the R toolbar MISC and then chose Change Working Directory. I was able to choose the directory that the .csv file was saved in. When I went back to the command line and typed getwd() the full directory was updated and correct and the read.csv function finally worked.
I had the same problem and when I checked the properties of the file on file explorer, it shows me the next message:
"Security: This file came from another computer and might be blocked to help protect this computer"
You click on the "Unblock" button and... you can access to the file from R without any problem, just using read.csv() function and from the directory specified as your working directory, even if is not the same as the file’s directory you are accessing to.
I just had this problem and I first switched to another directory and then switched back and the problem was fixed.
this work for me, accesing data from root. use double slash to access address.
dataset = read.csv('C:\\Users\\Desktop\\Machine Learning\\Data.csv')
Kindly check whether the file name has an extension for example:
abc.csv
if so remove the .csv extension.
set wd to the folder containing the file (~)
data<-read.csv("abc.csv")
Your data has been read the data object
In my case this very problem was raised by wrong spelling, lower case 'c:' instead of upper case 'C:' in the path. I corrected spelling and problem vanished.
You can add absolute path to the file
heisenberg <- read.csv(file="C:/Users/tiago/Desktop/sample_100000.csv")
If really want to run something like
heisenberg <- read.csv(file="sample_100000.csv")
then you'll have to change the working directory to match the place the .CSV file is at. More about it here.
Lately I'm having a strange problem with RStudio (v1.3.1056 on Ubuntu 18.04): When I try to open some text files, RStudio refuses with the message file is binary rather than text:
Yet, the file I'm trying to open is definitely a text file. As an example, take this bibtex file:
#misc{test,
author = {test},
year = {2018},
title = {test},
}
When I try to open it with the file name "test.bib", I get the error above. When renaming it to "test.txt" RStudio opens it without complaining. Here the steps as R code:
rstudioapi::navigateToFile("test.bib") # won't work
file.copy("test.bib", "test.txt", overwrite = TRUE)
rstudioapi::navigateToFile("test.txt") # works perfectly
I'm pretty sure that RStudio wouldn't mind the file ending and just try to open files as text no matter what in the past. But now I either have to rename the file or get a different text editor to edit my bib and other files.
As far as I can tell, this is not a problem of Ubuntu marking the file as binary. Otherwise one of these commands would complain, I think:
readLines("test.bib")
system("grep 'misc' test.bib")
The solution to this problem is rather stupid. Apparently it is possible in Linux to include newline characters in your folder name, yet either RStudio or file doesn't like that. I had no idea that my test.bib file was sitting in a folder with a newline character. So the problem can be reproduced with:
bib <- "#misc{test,
author = {test},
year = {2018},
title = {test},
}"
dir.create("test\nfolder")
writeLines(bib, "./test\nfolder/test.bib")
rstudioapi::navigateToFile("./test\nfolder/test.bib") # throws error
While it works when the folder is just called "test folder"! Sorry for wasting people's time, I should have just tested it elsewhere...
You can see the current test of whether a file is text or not here: https://github.com/rstudio/rstudio/blob/d1289249b11e0d12d2be12b3ceb701c41f110cec/src/cpp/session/SessionModuleContext.cpp#L1216. It looks for a recorded MIME type according to the filename extension (and .bib isn't in the list currently, so that will fail).
It then tries to run
file --dereference --mime --brief test.bib
and looks at the result. Maybe your system doesn't recognize test.bib as text/plain? A few other types would also be recognized as text; see the end of that function on github.
I have an excel file that I want to open in R. I tried both of these commands after saving the excel file as a csv file or a text file.
read.table() or read.csv()
I think part of the problem is where the file is located. I have it saved on the desk top. What am I missing here?
Here is the R output
In file(file, "rt") :
cannot open file 'Rtrial.csv': No such file or directory
> help.search("read.csv")
> read.csv("Rtrial.csv")
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
cannot open file 'Rtrial.csv': No such file or directory
> read.table("tab")
To throw out another option, why not set the working directory (preferably via a script) to the desktop using setwd('C:\John\Desktop') and then read the files just using file names
Try
f <- file.choose()
to choose the file interactively and save the name in f.
Then run read.csv on the saved filename
d <- read.csv(f)
Sound like you just have an issue with the path. Include the full path, if you use backslashes they need to be escaped: "C:\\folder\\folder\\Desktop\\file.csv" or "C:/folder/folder/Desktop/file.csv".
myfile = read.csv("C:/folder/folder/Desktop/file.csv") # or read.table()
It may also be wise to avoid spaces and symbols in your file names, though I'm fairly certain spaces are OK.
I had to combine Maiasaura and Svun answers to get it to work: using setwd and escaping all the slashes and spaces.
setwd('C:\\Users\\firstname\ lastname\\Desktop\\folder1\\folder2\\folder3')
data = read.csv("file.csv")
data
This solved the issue for me.
Here is one way to do it. It uses the ability of R to construct file paths based on the platform and hence will work on both Mac OS and Windows. Moreover, you don't need to convert your xls file to csv, as there are many R packages that will help you read xls directly (e.g. gdata package).
# get user's home directory
home = setwd(Sys.getenv("HOME"));
# construct path to file
fpath = file.path(home, "Desktop", "RTrial.xls");
# load gdata library to read xls files
library(gdata);
# read xls file
Rtrial = read.xls(fpath);
Let me know if this works.
Save as in excel will keep the file open and lock it so you can't open it. Close the excel file or you won't be able to use it in R.
Give the full path and escape backslashes read.csv("c:\\users\\JoeUser\\Desktop\\JoesData.csv")
I have experienced that this error occurs when you either move the excel file to the destination other than where your r file is located or when you move your r file to the destination other than where your excel file is located.
Good Practice:
Keep your .r and .csv files in the same directory.
open your .r file from getting into its directory instead of opening the r file from rstuio's open file option.
You also have import Dataset option at Environment Block, just click there and get your required packages installed & from next time use this option to read datasets. You will not get this error again.
I also appreciate the above provided answers.
Another way of reading Excel including the new format xlsx could be the package speedR (https://r-forge.r-project.org/projects/speedr/). It is an interactive and visual data importer. Besides importing you can filter(subset) the existing objects from the R workspace.
My issue was very simple, the working directory was not the "Source" directory that was printed when the file ran. To fix this, you can use getwd() and setwd() to get your relative links working, or just use a full path when opening the csv.
print(getwd()) # Where does the code think it is?
setwd("~/Documents") # Where do I want my code to be?
dat = read.csv("~/Documents/Data Visualization/expDataAnalysis/one/ac1_survey.csv") #just make it work!
MAC OS It happened to me as well. I simply chose from the R toolbar MISC and then chose Change Working Directory. I was able to choose the directory that the .csv file was saved in. When I went back to the command line and typed getwd() the full directory was updated and correct and the read.csv function finally worked.
I had the same problem and when I checked the properties of the file on file explorer, it shows me the next message:
"Security: This file came from another computer and might be blocked to help protect this computer"
You click on the "Unblock" button and... you can access to the file from R without any problem, just using read.csv() function and from the directory specified as your working directory, even if is not the same as the file’s directory you are accessing to.
I just had this problem and I first switched to another directory and then switched back and the problem was fixed.
this work for me, accesing data from root. use double slash to access address.
dataset = read.csv('C:\\Users\\Desktop\\Machine Learning\\Data.csv')
Kindly check whether the file name has an extension for example:
abc.csv
if so remove the .csv extension.
set wd to the folder containing the file (~)
data<-read.csv("abc.csv")
Your data has been read the data object
In my case this very problem was raised by wrong spelling, lower case 'c:' instead of upper case 'C:' in the path. I corrected spelling and problem vanished.
You can add absolute path to the file
heisenberg <- read.csv(file="C:/Users/tiago/Desktop/sample_100000.csv")
If really want to run something like
heisenberg <- read.csv(file="sample_100000.csv")
then you'll have to change the working directory to match the place the .CSV file is at. More about it here.
I have a set of SAS data sets and I want to open it using Excel or R. I don't have a SAS software with me so i can't use the export option in it. Is there any converter that converts from SAS7BDAT to excel?
Thanks
I help develop the Colectica for Excel addin, which opens SAS data files in Excel. No SAS software or ODBC configurations are required. The addin directly reads the SAS file and then inserts the data and metadata into your worksheet.
Imports SAS .sas7bdat data and column names
Imports SAS .sas7bcat formats and value labels when avalaible
The Excel addin is downloadable from http://www.colectica.com/software/colecticaforexcel
Documentation is available in the user manual.
You could use SAS add in for Microsoft office to open the SAS dataset in Excel. Not sure if it is free though.
http://support.sas.com/software/products/addin/
As Reese suggested you can use - SAS Universal Viewer , its free!!
Here is the link :-
https://support.sas.com/downloads/browse.htm?fil=&cat=74
Or you can download SAS University Edition, which is also free, it is more than just a viewer, you can write and execute programs in here.
http://www.sas.com/en_us/software/university-edition/download-software.html
Here a quick-and-dirty python five-liner to convert a .xpt file to .csv
import pandas as pd
FILE_PATH = "(directory containing file)"
FILE = "ABC" # filename itself (without suffix)
# Note: might need to substitute the column name of the index (in quotes) for "None" here
df = pd.read_sas(FILE_PATH + FILE + '.XPT', index=None)
df.to_csv(FILE_PATH + FILE + '.csv')
Hopefully this might help someone
I came across the same "need" and after some research here and there, I found a nice and easy way with R and the latest version of RStudio (as per 2020 June date - the FREE one). Using it, you can open various formats of files and RStudio generates for you the R script it ran behind. You can use this as a starting point, in order to have the .sas7bdat file opened, and then do the conversion step.
Steps to follow in order to import the file using the RStudio "visual" way: Evironment tab -> Import Dataset -> From SAS...
It will ask you to import the haven library. After the installation you will have a tab with the preview of the data within the file and also the R script ran behind which will look like this:
library(haven)
aux <- read_sas("//PATH_ON_YOUR_MACHINE_TO_FILE/actual_file.sas7bdat", NULL)
View(aux)
Notice the NULL there, it has the purpose of converting empty strings to NULL.
But wait, we also need to convert it to a .csv file in order to have the final job done. For this you simply add below those lines from above the following:
write.csv(aux, "actual_file.csv")
Which will produce within the same folder with the original SAS file, the desired .CSV one. If you want to have ";" as separator instead on "," use write.csv2(aux, "actual_file.csv"). Anyway Strings are enclosed by " " so it should be fine.